This sequencing impulse is helping scientists map out in more detail the mutational landscape of coronaviruses circulating around the country. Therefore, it is not surprising that they begin to generate more surprises. But as the pace of genomic data generation has accelerated, there has not yet been a similar, concerted advance in what is called “variant characterization”.
Sequencing can help you identify mutations that I could be problematic. But it can’t tell you if these mutations cause the virus version to behave differently than others. To do this, you must perform studies with antibodies, living human cells and animal models. Each type of experiment or analysis requires a unique set of skills and there are many different methods for measuring the same things. You also need immunologists, structural biologists, virologists and a lot of other -ologists. And ideally, you want them to meet the same scientific standards so you can compare one variant with the next and determine if a new strain is worrying from a public health standpoint or just interesting.
In the United States, the CDC is the main body with authority to designate emerging strains as “variants of interest” or “variants of concern.” Crossing this threshold requires strong evidence that a given constellation of mutations confers the ability to do any of the following four things: spread more quickly and easily, cause more serious illness, weaken the effectiveness of Covid-19 treatments or evade antibodies produced from vaccination. or during a previous infection with an earlier version of the virus.
So far, the agency has only elevated three new versions of SARS-CoV-2 to the most troubling category: B.1.1.7, which was first detected in the UK, B.1.351 from South Africa and P .1 of Brazil. . (Although there is an ongoing struggle over which code naming system to use, most scientists have agreed to avoid the “insert-place-name-here” nomenclature because of its inaccuracy and stigmatizing effect. To simplify, we we will refer to B.1.1.7, B.1.351 and P.1 hereafter as Big Three.)
But the agency is currently tracking additional interest variants, including B.1.256 in New York and B.1427 / 429 in California, and is maintaining ongoing studies to assess the ability of these strains to evade. immune responses and erode the protections offered by existing vaccines. As new data becomes available, the agency may increase any particularly worrying variant of this higher level. “The threshold for designating a variant of interest should be relatively low to control potentially important variants,” a CDC spokesman told WIRED by email. “However, the threshold for designating a variant of concern should be high to focus resources on variants with the highest public health implications.”
The spokesman did not provide details on what the agency considers “strong evidence,” but said the CDC has been involved with international partners, including the World Health Organization, in the debate over the criteria for designating variants.
In other words, it’s not just about finding new variants, it’s about characterizing their biological behavior: what does it mean for someone to become infected with one another? “Getting sequences is just the beginning of the story,” Topol says. “There’s a lot more science that has to go into whether a mutation is significant. And right now, a lot of labs that post about it are just looking at a part of the story, because that’s the fastest. But what’s fast too it can be misleading. ”
For example, several studies conducted in recent weeks have shown that antibodies trained to attack older versions of the virus have much more difficulty recognizing variants B.1.351 and P.1. This means alarms about the effectiveness of vaccines. But just because antibodies don’t fight these new mutants in a test tube doesn’t mean your immune system has the same problems in a fight against the real-world boss. The immune system is more than antibodies and far fewer laboratories have the experience to perform tests with live T cells, the other major player in the development of Covid-19 immunity. These cells, which eliminate the virus, eliminating herds of infected cells, are capricious to grow outside the human body. Therefore, it has taken a little longer to understand how they respond to variants. But new data suggests they respond well.